Can't remember the exact date HMRC gave, but there used to be an automated message when calling the Employer's helpline that said they would only deal with 18/19 CIS refunds towards the end of September.

Now dont all shout at me but apparently according to HMRC this problem wont be present under MTD - you'll be able to see all taxes in one place and do your own set off if overpaid on one tax and want to use for another or client has used the wrong ref nos and paid VAT instead of CT for example.
Any other benefits of MTD? No.. didnt think I'd get any answer.